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Posts about scientific research and development as well as science and engineering breakthroughs.
Recommended posts: R&D Spending in USA Universities - Diplomacy and Science Research - Research Career in Industry or Academia - New Understanding of Human DNA - Basic Science Research Funding - The Worlds Best Research Universities - Mystery of High-Temperature Superconductivity - Why Most Published Research Findings Are False

Using Scientific Knowledge to Drive Policies that Create a Better World

I have written about the problems of overfishing in the past: Add Over-Fishing to the Huge Government Debt as Examples of How We Are Consuming Beyond Our Means (2012)Fishless Future (2006)North American Fish Threatened (2008)The State of the Oceans is Not Good (2011)European Eels in Crisis After 95% Decline in Last 25 years (2009). This is not a complicated problem. If you just pay attention to the science and make wise decisions with an understanding of systems we can improve the situation.

And the USA has done so. The USA has more work to do, but by taking sensible steps based on an understanding of science we have made significant progress.

How the world can stop overfishing – A case study of U.S. fishery success

By 1996, the US had declared 86 species overfished. Fast forward twenty years, and only 29 species in US waters are classified as overfished. That’s a decrease of 66% from the peak of overfishing in the 1990s.

One year after President Clinton declared the New England ground fishery a federal disaster, congress met in Washington to amend and renew the 20-year-old Fishery Conservation and Management Act. The result was the Magnuson-Stevens Act, a major bipartisan commitment to end overfishing in US waters and promote fish stock recovery.

The goal of the Magnuson-Stevens Act was to create a framework for rebuilding overfished stocks in as short a time as possible. The timeframe for rebuilding a fish stock under the act is typically ten years or less.

To accomplish such a goal, scientists established fishery management plans for each overfished stock and instituted annual catch limits to control overfishing.

By the end of 2015, 89% of fisheries with annual catch limits in place had halted overfishing.

While 64% of the fish stocks managed by the Magnuson-Stevens Act are now rebuilt or recovering, success hasn’t been universal. Certain regional fisheries, such as those in the Gulf of Mexico and New England, have struggled to control overfishing under existing regulations. The act also does a poor job of protecting highly migratory species, such as tuna, swordfish, and sharks, which move freely between different regulatory areas.

We need to build on our successful use of scientific knowledge to make wise decisions and implement wise government policy. Sadly there is an alarming lack of appropriate thinking by many of those we elect to office, in the USA and around the globe. We can’t afford to elect people that don’t have an understanding of how to make wise decisions and how to ensure scientific knowledge forms the basis of policy when it should, such as: overfishing, pollution, global warming, the health care benefits vaccines provide when they are used properly, the dangers of abusing antibiotics, etc..

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The Amazing Reality of Genes and The History of Scientific Inquiry

cover of The Gene

The Gene by Siddhartha Mukherjee is a wonderful book. He does a great job of explaining the history of scientists learning about genes as well as providing understandable explanations for the current scientific understanding of genes and how they impact our lives.

As I have mentioned before, I find biology fascinating even though I found biology classes utterly boring and painful. I wish everyone could learn about biology with the insight people like Siddhartha Mukherjee provide. I realize not everyone is going to find the history and understanding of genes to be fascinating but for those who might this book is a great read. And don’t rule the idea out just because you found biology classes painful.

Life may be chemistry, but it’s a special circumstance of chemistry. Organisms exist not because of reactions that are possible, but because of reactions that are barely possible. Too much reactivity and we would spontaneously combust. Too little, and we would turn cold and die. Proteins enable these barely possible reactions, allowing us to live on the edges of chemical entropy – skating perilously, but never falling in.
– page 134

Whether it is the physics of our solar system or our biology there is a precarious band that allowed beings such as ourselves to evolve.

most genes, as Richard Dawkins describes them, are not “blueprints” but “recipes.” They do not specify parts, but processes; they are formulas, not forms. If you change a blueprint, the final product is change in a perfectly predictable manner: eliminate a widget specified in the plan, and you get a machine with a missing widget. But alteration of a recipe or formula doesn’t not change the product in a predictable manner: if you quadruple the amount of butter in a cake, the eventual effect is more complicated than just a quadruply buttered cake (try it; the whole thing collapses in an oily mess).
– page 454

The is a powerful idea. And when combined with turning genes on and off it is understandable how complex determining genetic impacts on biology and disease are. A few diseases or results (e.g. blue eyes) are nearly as simple as 1 or a few genes being altered in a specific way but most are not nearly so easy. And it isn’t like even that is so easy but with the amazing efforts scientists have made and the advanced tools those scientists created it can now seem simple to identify some such diseases.

The genetic code is universal. A gene from a blue whale can be inserted into a microscopic bacterium and it will be deciphered accurately and with near perfect fidelity. A corollary: there is nothing particularly special about human genes.
– page 480

This is something I have known and understood but it is still amazing. Genes and proteins and how they act to create the incredible diversity of life is something that is awe inspiring.

This book is a wonderful adventure for those interested in life and scientific inquiry.

Related: Epigenetics, Scientific Inquiry and UncertaintyHuman Gene Origins: 37% Bacterial, 35% Animal, 28% EukaryoticUnexpected Risks Found In Editing Genes To Prevent Inherited DisordersEpigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeWhy Don’t All Ant Species Replace Queens in the Colony, Since Some Do

Eating Nuts May Reduce the Risk of Heart Disease, Cancer and Other Diseases

A large analysis of current research shows that people who eat at least 20g of nuts a day have a lower risk of heart disease, cancer and other diseases. The analysis of all current studies on nut consumption and disease risk has revealed that 20g a day – equivalent to a handful – can cut people’s risk of coronary heart disease by nearly 30%, their risk of cancer by 15%, and their risk of premature death by 22%.

While this is reassuring news to those of us (like me) that frequently eat nuts I am not sold on their evidence. Heath research is prone to overstating the benefits. Still there is little reason to avoid making nuts part of a healthy diet. That is a big part of the reason I have. They offer benefits and maybe even great ones (as indicated in this research) without much risk.

An average of at least 20g of nut consumption was also associated with a reduced risk of dying from respiratory disease by about a half, and diabetes by nearly 40 percent, although the researchers note that there is less data about these diseases in relation to nut consumption.

The study, led by researchers from Imperial College London and the Norwegian University of Science and Technology, is published in the journal BMC Medicine, Nut consumption and risk of cardiovascular disease, total cancer, all-cause and cause-specific mortality: a systematic review and dose-response meta-analysis of prospective studies (open access paper).

The research team analysed 29 published studies from around the world that involved up to 819,000 participants, including more than 12,000 cases of coronary heart disease, 9,000 cases of stroke, 18,000 cases of cardiovascular disease and cancer, and more than 85,000 deaths.

While there was some variation between the populations that were studied, such as between men and women, people living in different regions, or people with different risk factors, the researchers found that nut consumption was associated with a reduction in disease risk across most of them.

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Chimpanzees Solving Numerical Memory Test Better Than People

I can’t even see all the numbers before they disappear. But chimpanzees are shown seeing a flash of 9 numbers on a screen and then pointing to where they were on the screen in order from 1 to 9. Human test subjects can’t even do 5 numbers most of the time.

Related: Chimpanzees Use Spears to Hunt Bush BabiesOrangutan Attempts to Hunt Fish with SpearCrows can Perform as Well as 7 to 10-year-olds on cause-and-effect Water Displacement TasksTropical Lizards Can Solve Novel Problems and Remember the Solutions

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The Challenge of Protecting Us from Evolving Bacterial Threats

I have long been concerned about the practices we continue to use increasing the risks of “superbugs.” I have written about this many times, including: The Overuse of Antibiotics Carries Large Long Term Risks (2005)Are you ready for a world without antibiotics? (2010), Antibiotics Breed Superbugs Faster Than Expected (2010), Entirely New Antibiotic (platensimycin) Developed (2006), Our Poor Antibiotic Practices Have Sped the Evolution of Resistance to Our Last-Resort Antibiotic (2015).

I do also believe the wonderful breakthroughs we make when we invest in science and engineering have made our lives much better and have the potential to continue to do so in many ways, including in dealing with the risks of superbugs. But this is something that requires great effort by many smart people and a great deal of money. It will only happen if we put in the effort.

Winning war against ‘superbugs’

hey won this particular battle, or at least gained some critical intelligence, not by designing a new antibiotic, but by interfering with the metabolism of the bacterial “bugs” — E. coli in this case — and rendering them weaker in the face of existing antibiotics

ROS, or “reactive oxygen species,” include molecules like superoxide and hydrogen peroxide that are natural byproducts of normal metabolic activity. Bacteria usually cope just fine with them, but too many can cause serious damage or even kill the cell. In fact, Collins’ team revealed a few years ago the true antibiotic modus operandi: they kill bacteria in part by ramping up ROS production.

We need to continue to pursue many paths to protecting us from rapidly evolving bacterial risks. Many promising research results will fail to produce usable solutions. We need to try many promising ideas to find useful tools and strategies to protect human health.

Promoting Open Science

As I have written many times in the past we need to take back science from the closed-science journals. Historically journals were useful (before the internet). With the advent of the internet (and its spread) instead of maintaining the mission they started with the journals sought to maximize their profit and their own pay and jobs at the expense of sharing scientific knowledge with the world.

Elsevier — my part in its downfall by Timothy Gowers provides another good look at what can be done to promote science, math and engineering by addressing the damage to that goal being done by closed science publishers.

Recently he announced the launch of Discrete Analysis, a new journal that publishes to arXiv.

Disrupting the subscription journals’ business model for the necessary large-scale transformation to open access from the Max Planck Digital Library provides some good ideas for how to promote science in spite of the closed science journals fighting that goal.

There needs to be a shared understanding that the money currently locked in the journal subscription system must be withdrawn and re-purposed for open access publishing services. The current library acquisition budgets are the ultimate reservoir for enabling the transformation without financial or other risks.

Related: The Architecture of Access to Scientific KnowledgeWhy Copyright Extension is a Very Bad IdeaPublishers Continue to Fight Open Access to Science (2007)Harvard Steps Up Defense Against Abusive Journal Publishers (2012)

An Eukaryote that Completely Lacks Mitochondria

If you don’t have any idea what the title means that is ok. I probably wouldn’t have until the last 15 years when I found how interesting biology is thanks to the internet and wonderful resources online making biology interesting. I hope you find learning about biology as interesting as I do.

Look, Ma! No Mitochondria

Mitochondria have their own DNA, and scientists believe they were once free-living bacteria that got engulfed by primitive, ancient cells that were evolving to become the complex life forms we know and love today.

What they learned is that instead of relying on mitochondria to assemble iron-sulfur clusters, these cells use a different kind of machinery. And it looks like they acquired it from bacteria.

The researchers say this is the first example of any eukaryote that completely lacks mitochondria.

However, the results do not negate the idea that the acquisition of a mitochondrion was an important and perhaps defining event in the evolution of eukaryotic cells, he adds.

That’s because it seems clear that this organism’s ancestors had mitochondria that were then lost after the cells acquired their non-mitochondrial system for making iron-sulfur clusters.

Biology is amazing and mitochondria are one of the many amazing details. I wish so much that my education could have given biology a tiny fraction of the interest I have found it in after school.

Related: Human Gene Origins: 37% Bacterial, 35% Animal, 28% EukaryoticOne Species’ Genome Discovered Inside Another’sParasite Evolved from Cnidarians (Jellyfish etc.)Plants, Unikonts, Excavates and SARs

Healthy Living Greatly Reduces Likelihood of Dying from Cancer

Lifestyle choices can greatly reduce the incidence and death rates from cancer. 4 factors can reduce the incidence of cancer by up to 40% and death rate by 50%: don’t smoke, don’t drink alcohol in excess, maintain a BMI between 18.5 and 27.5, and exercising at a moderate intensity for at least 150 minutes or at a vigorous intensity for at least 75 minutes every week.

Preventable Incidence and Mortality of Carcinoma Associated With Lifestyle Factors Among White Adults in the United States

A substantial cancer burden may be prevented through lifestyle modification. Primary prevention should remain a priority for cancer control.

Cancer is the second leading cause of death in the United States, with 1.6 million new cancer cases and 0.6 million cancer deaths projected to occur in 2016.1 The cancer mortality rate, age-standardized to the 2000 US standard population, decreased from 199 to 163 per 100 000 between 1969 and 2013.2 However, this decline (17.9%) has been modest compared with the dramatic decrease in heart disease mortality (67.5%) during the same period, highlighting the need for further efforts in cancer prevention and treatment.

The study reviewed previous studies and the makeup of the previous studies and available statistics. As they state in the paper: “Because our cohorts’ participants were predominantly whites, to avoid any influence of different racial distributions on the comparison with the general population, we only included whites in the analysis.” They also excluded about 10% of cancers that are believed to have strong environmental factors.

Table Showing a Comparison of Lifestyle Factors in the Low- and High-Risk Groups

In the 2 cohort studies of US white individuals, we found that overall, 20% to 40% of carcinoma cases and about half of carcinoma deaths can be potentially prevented through lifestyle modification. Not surprisingly, these figures increased to 40% to 70% when assessed with regard to the broader US population of whites, which has a much worse lifestyle pattern than our cohorts.

Notably, approximately 80% to 90% of lung cancer deaths could be avoided if Americans adopted the lifestyle of the low-risk group, mainly by quitting smoking. For other cancers, from 10% to 70% of deaths could be prevented. These results provide strong support for the importance of environmental factors in cancer risk and reinforce the enormous potential of primary prevention for cancer control.

Related: A Healthy Lifestyle is More About Health Care than the Sickness Management That We Call Health Care IsBetter Health Through: Exercise, Not Smoking, Low Weight, Healthy Diet and Low Alcohol Intake (2013)Exercise Is Really Really Good for YouPhysical Activity for Adults: Inactivity Leads to 5.3 Million Early Deaths a Year (2012)

International Science Research Scholar Grants

The Howard Hughes Medical Institute (HHMI), Bill & Melinda Gates Foundation, Wellcome Trust, and Calouste Gulbenkian Foundation have announced the International Research Scholars Program which aims to support up to 50 outstanding early career scientists worldwide. The program’s aim is to help develop scientific talent worldwide.

The new international competition is seeking top early career researchers from a wide variety of biomedical research fields. Applicants must have started their first independent research position on or after April 1, 2009. Awardees will be invited to participate in research meetings with scientists supported by the funders. These meetings facilitate the exchange of ideas, stimulate new research, and provide an opportunity for collaborative endeavors within the international scientific community.

  • Awardees will receive a total of $650,000 over five years.
  • Applications are due June 30, 2016.
  • Awardees will be notified in April 2017.

HHMI and its partners have committed a total of $37.4 million for the International Research Scholars Program and will award each scientist who is selected a total of $650,000 over five years. The competition is open to scientists who have trained in the U.S. or United Kingdom for at least one year. Additionally, eligible scientists must have run their own labs for less than seven years, and work in one of the eligible countries.

Nieng Yan

Although Nieng Yan had several grants when she started her lab at Tsinghua University in 2007, she barely had enough money to pay her eight lab members. “In China, there is a limit on the percentage of a grant that you can use to pay people — your graduate students, your postdocs, your technicians, your assistants — to a decent level,” she explains. After struggling to balance her budget for several years, Yan’s scientific achievements and potential landed her an international grant from HHMI in 2012. “The amount of money provided by Hughes is relatively small compared to other programs, but it has the advantage that you can freely decide what to do with it,” says Yan. In fact, HHMI’s science officers encouraged Yan to use her five-year International Early Career Award (IECS) to cover the cost of paying her lab team, explaining that the money could be used in any way that assisted her research. Today, Yan has 15 people working in her lab helping to elucidate the structures of proteins that move molecules in and out of cells. The protein channels and transporters they study are mutated in a number of diseases — including diabetes and cancer — and understanding how they work could help in the development of drugs that block their ill effects. For example, the team recently solved the structure of GLUT1 – a glucose transporter that is often overexpressed in malignant tumor cells. Their data may provide clues for how to inhibit the transporter and perhaps even reveal a way to use it to deliver chemotherapeutic drugs. Photo Credit: Kevin Wolf (AP)

Countries that are not eligible for this competition include the G7 countries (Canada, France, Germany, Italy, Japan, United Kingdom and United States), as well as countries identified by the U.S. Department of Treasury, Office of Foreign Assets Control (OFAC) as being subject to comprehensive country or territory-wide sanctions or where current OFAC regulations prohibit U.S. persons or entities from engaging in the funding arrangements contemplated by this grant program. For this program, such sanctioned countries or territories currently include Iran, North Korea, Sudan, Syria, and the Crimea region of Ukraine.

Related: Directory of Science and Engineering Scholarships and FellowshipsFunding Sources for Independent Postdoctoral Research Projects in BiologyScientific Research Spending Cuts in the USA and Increases Overseas are Tempting Scientists to Leave the USA (2013)HHMI Expands Support of Postdoctoral Scientists (2009)Science, Engineering and Math Fellowships

Medicinal Plants

Another great webcast from SciShow. In this webcast Hank Green discusses how we have used plants to treat us and improve our health.

In the webcast, Hank also does a good job touching a bit on the scientific inquiry process (which is something I find interesting and I think is very important for people living in society today to understand).

Related: Youyou Tu, The First Chinese Woman to Win a Nobel PrizeRubber TreesPhotosynthesis: Science Explained

Gut Bacteria Explored as Medical Treatment – even for Cancer

The interaction between gut bacteria and human health continues to be a fertile area of medical research. It appears to be in the very early days of such research. Of course, as I have said before, headline making news often doesn’t result in medical breakthrough, and even when it does a decade isn’t a long wait for it to happen.

How Gut Bacteria Are Shaking Up Cancer Research

In November, University of Chicago researchers wrote that giving mice Bifidobacterium, which normally resides in the gastrointestinal tract, was as effective as an immunotherapy in controlling the growth of skin cancer. Combining the two practically eliminated tumor growth. In the second study, scientists in France found that some bacterial species activated a response to immunotherapy, which didn’t occur without the microbes.

The complex interactions involved in human health is another area that has huge room for research going forward.

Related: Some Bacteria Might Fight Cancer (2008)Cancer Vaccines (2011)Using Diatom Algae to Deliver Chemotherapy Drugs Directly to Cancer Cells (2015)Webcast of a T-cell Killing a Cancerous Cell (2012)

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